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In the anime

Abilities have been shown in the anime, but are usually only used in battles; however, sometimes they have an effect on the plot, such as Ash's Infernape's Blaze. Abilities sometimes work differently in the anime than they would in the games, such as Mold Breaker, which in the anime cancels out more Abilities than it would in the games.

In the original series

The only Ability that was seen in the original series was Color Change, being used by Madison and Alexa's Kecleon in The Kecleon Caper. It was later used by Harrison's Kecleon in Playing With Fire!.

In the Advanced Generation series

The first Ability to be seen other than Color Change was Rough Skin, first seen in Sharpedo Attack!. It was used by a wild Sharpedo.
In Now That's Flower Power! a Kecleon used Color Change.
In A Poké-BLOCK Party!, a Whismur used its Soundproof Ability to stay awake and listen to Jigglypuff's song.
Colonel Hansen's Shedinja used Wonder Guard in The Princess and the Togepi.
Two Abilities were seen in Balance of Power, being used by Ash's Pikachu and Grovyle, using Static and Overgrow respectively.
Bart's Castform used Forecast in Unfair Weather Friends, turning into its Sunny and Rainy Form.
In The Garden of Eatin', Marcel's Vigoroth used Vital Spirit.
Both Drizzle and Drought were seen in Gaining Groudon and The Scuffle of Legends respectively.
In It's Still Rocket Roll to Me!, Liza's Lunatone used Levitate.
In Eight Ain't Enough, Juan's Luvdisc used Swift Swim.
In Showdown At Linoone, a Linoone has the Ability Pickup and takes items to its private stash, including May's Poké Balls.
In At the End of the Fray, Tyson's Hariyama used Thick Fat.
In Rough, Tough Jigglypuff, Lisa Mitchum's Jigglypuff used Cute Charm Her father's Loudred used Soundproof to stop Jigglypuff's Sing from working.
Angela's Kecleon used Color Change in From Cradle to Save, as well as Brock's Bonsly using Rock Head.
In Pinch Healing!, a wild Wooper used Water Absorb.
In Once More With Reeling!, May's Blaziken used its Blaze Ability while Ash's Sceptile used Overgrow during their Contest Battle in the Terracotta Contest.

In the Diamond & Pearl series

Abilities proved important in the battles Paul and Ash had with Roark. During Paul's battle in Shapes of Things to Come!, his Elekid uses Static to paralyze Roark's Onix and Cranidos although the latter shakes it off with Mold Breaker. Paul also deliberately allows his Chimchar to take extra damage so that it can activate Blaze. After Ash's first match with Roark ends in defeat, Brock briefly lends him Sudowoodo in Wild in the Streets! because its Ability Rock Head makes it similar to Roark's Pokémon Onix, who also had the Ability. During Ash's rematch in O'er the Rampardos We Watched!, Pikachu also activates Static against Roark's newly evolved Rampardos and it is similarly ineffective.
In A Secret Sphere of Influence!, Officer Jenny's Stunky used Stench.
Gardenia's Cherubi caught Ash by surprise during their first battle in The Grass Menagerie! when it was able to move very quickly with Chlorophyll.
In Tag! We're It...!, Ash and Paul found themselves at a disadvantage during their first Tag Battle in the Hearthome City Tag Battle Competition because the Rhydon used by one of their opponents possessed Lightning Rod, rendering Pikachu's Electric-type attacks useless.
In Glory Blaze! Ash, Dawn and Brock found Paul and his other Pokémon evidently abusing his Chimchar, repeatedly attacking it until it eventually collapsed from exhaustion. When confronted, Paul explained that Chimchar actually wanted the brutal training regimen; when they first met, Chimchar was being attacked by wild Zangoose and when pushed to the limit it activated Blaze and defeated all of the Zangoose with Flame Wheel. This incredible power was what drove Paul to capture Chimchar in the first place and the two have been trying to replicate the experience ever since with no success.
Swift Swim was an important part of Ash's Buizel going toe to toe with Maylene's Lucario in A Triple Fighting Chance!
Blaze returned in Chim - Charred! when Ash's Chimchar became enraged during a battle with Paul's Ursaring. It took considerable effort for Ash to return Chimchar to normal after it defeated Ursaring, causing Paul to leave the battle a draw. Paul told Ash that they would only battle again when and if Ash and Chimchar learned to control Blaze.
In Battling the Generation Gap!, Lila's Delcatty activated his Cute Charm Ability while battling Dawn's Ambipom in the final round of the Celestic Contest.
Brock's Croagunk first used his Anticipation Ability in Losing Its Lustrous!. He often used it to find Team Rocket and chase them off on his own.
Two Darkrai have used Bad Dreams. One used it in The Rise of Darkrai and another in Sleepless in Pre-Battle!.
In A Shield with a Twist!, Fantina's Gengar used Levitate.
In Dealing with Defensive Types!, Byron's Bronzor used its Heatproof Ability to minimize damage from Ash's Chimchar's Flamethrower.
In Another One Gabites the Dust!, Jessie's Yanmega activated its Speed Boost Ability while performing in the Chocovine Contest.
In Pursuing a Lofty Goal!, Paul's Honchkrow used its Ability Super Luck.
In Sliding Into Seventh!, Jeremiah's Skuntank was known to have Stench as it Ability but the Ability activated off-screen.
In Evolving Strategies!, Paul's Magmortar used its Flame Body Ability to burn Ash's Pikachu. Paul's Ursaring also used its Guts Ability when Ash's Pikachu's Static activated.
An Arceus used Multitype in Arceus and the Jewel of Life.
In Challenging a Towering Figure!, Palmer's Rhyperior used Solid Rock.
A wild Trapinch used its Arena Trap Ability in A Rivalry to Gible On!.
A wild Heatran used Flash Fire in Pokémon Ranger: Heatran Rescue!.
Volkner's Electivire used its Motor Drive Ability in The Eighth Wonder of the Sinnoh World! against Ash in their Gym battle. It was later used by Paul's Electivire in Battling a Thaw in Relations!.
In Casting a Paul on Barry!, Barry's Empoleon activated its Torrent Ability while battling Paul's Electivire in the third round of the Lily of the Valley Conference.
Paul's Aggron used its Rock Head Ability in Familiarity Breeds Strategy! to avoid damage from its Double-Edge attack. In the next episode Paul's Froslass and Ninjask used Snow Cloak and Speed Boost respectively.
Illusion was seen twice in Zoroark: Master of Illusions, being seen by a Zoroark and Zorua.

In the Best Wishes series

A Hidden Ability was first seen in Saving Darmanitan From the Bell! by a Darmanitan using Zen Mode.
In A Rival Battle for Club Champ!, Trip's Tranquill used Super Luck to easily defeat Ash's Oshawott and Tepig. Trip's Frillish later used Cursed Body.
In Here Comes the Trubbish Squad!, a wild Trubbish used its Ability Stench.
In A Night in the Nacrene City Museum!, Lenora's Watchog used its Illuminate Ability to reveal any hidden things in the museum to appear.
Sewaddle was revealed to have Swarm in A Connoisseur's Revenge! but he wasn't shown activating it. Cilan's Dwebble was shown using its Sturdy Ability in the same episode.
A wild Venipede used its Poison Point Ability to poison Ash in A Venipede Stampede!.
In Gotta Catch A Roggenrola!, Iris pointed out that Roggenrola had the Ability Sturdy, implying that Roggenrola would receive less damage than a Pokémon normally would.
Luke's Zorua often used Illusion to help Luke in making his movies. It was first seen in Movie Time! Zorua in "The Legend of the Pokémon Knight"!.
In The Club Battle Hearts of Fury: Emolga Versus Sawk!, Iris's Emolga used Static to help it win a battle against Stephan's Sawk.
In Enter Elesa, Electrifying Gym Leader!, Bianca's father's Red Flash Darmanitan used Zen Mode.
Three Darmanitan used Zen Mode in A Maractus Musical!.
In Scraggy and the Demanding Gothita!, a wild Garbodor used Stench.
In A Call for Brotherly Love!, Chili's Pansear used its Gluttony Ability.
In Battling the King of the Mines!, Ash's Boldore used its Sturdy Ability to stop a Horn Drill from working.
In The Clubsplosion Begins!, Edmund's Seismitoad used Swift Swim against Stephan's Sawk, but ended up losing.
In Goodbye, Junior Cup - Hello Adventure!, Alder's Bouffalant used Sap Sipper to defeat Trip's Serperior.
In The Road to Humilau!, Marlon's Jellicent used Cursed Body.
Swarm wasn't seen until Strong Strategy Steals the Show! during Leavanny's battle with Stephan's Sawk.
In The Island of Illusions!, a Zoroark used Illusion.
In Survival of the Striaton Gym!, Morana's Abomasnow used its Snow Warning Ability. Cilan's Pansage was confirmed to have Gluttony as his Ability in the same episode.

In the XY series

Clemont's Chespin used its Ability Overgrow in An Appetite for Battle! battling against a Delphox.
In Mega Evolution Special I, Siebold's Mega Blastoise was shown to have Mega Launcher.
Both Dark Aura and Fairy Aura were seen in Diancie and the Cocoon of Destruction.
Ramos's Jumpluff and Weepinbell were both shown to have Chlorophyll as their Ability in The Green, Green Grass Types of Home!.
Ash's Goodra used its Ability Hydration in Ash's Gym battle against Clemont in The Moment of Lumiose Truth!.
Ash's Fletchinder used its Flame Body Ability in A Not-So-Flying Start! to help hatch an Egg that his Hawlucha found.
Olympia's two Meowstic were seen using their respective Abilities in All Eyes on the Future!, with the male Meowstic having its Hidden Ability Prankster and the female one having Keen Eye.
Two Abilities were seen in Mega Evolution Special IV, both in battle against Alain's Charizard. A Mega Venusaur used Thick Fat to half the damage it took from a Flamethrower. Malva's Houndoom later used Flash Fire to absorb another Flamethrower.

In the manga

In the Be the Best! Pokémon B+W manga

Pokémon Ranger's Zebstrika activating Lightningrod in Be the Best! Pokémon B+W
Monta's Roggenrola activated Sturdy in The Key to Triple Battles.
A Pokémon Ranger's Zebstrika and Monta's Excadrill activated Lightningrod and Sand Force in The Battle for More Friends!.
Dol's Bouffalant activated Sap Sipper in Challenge the Battle Subway!.
Monta's Watchog activated Illuminate in Let's Master Pokémon Capturing!.
Monta's Victini was unable to activate Victory Star in The Birth of the Best Pokémon Trainer! since the Serperior Cheren borrowed used Gastro Acid.
In the movie adaptations
Darkrai activated Bad Dreams in The Rise of Darkrai.
Xerneas activated Fairy Aura in Diancie and the Cocoon of Destruction.

In the Pokémon Adventures manga

Ruby & Sapphire chapter

Brawly's Makuhita activating Thick Fat in Pokémon Adventures
Parallel to their introduction in Generation III of the video games, Abilities were first introduced in the Ruby & Sapphire chapter of Pokémon Adventures.
During Sapphire's battle with Roxanne in Blowing Past Nosepass I, Roxanne's Nosepass proved superior to Rono. Worried that Rono would be defeated, Sapphire attempted to switch Rono out for Chic but was unable to. Roxanne explained that because her Nosepass has Magnet Pull, Steel-type Pokémon cannot switch out. However, Sapphire figured out in the next round that she could use this to her advantage because Nosepass's magnetic attunement causes it to automatically face north when idle. While Roxanne was bragging about her impending victory, Nosepass let its guard down, allowing Rono to sneak up behind it from the south and land a devastating hit that caused Nosepass to faint.
Ruby's first encounter with Abilities arrived in Stick This in Your Craw, Crawdaunt II when he and Mr. Briney were attacked by a wild Crawdaunt. Peeko tried to defeat it with Quick Attack, but the Crawdaunt's Shell Armor prevented it from doing much damage at all. After Mr. Briney fell unconscious, Ruby had Kiki use Double-Edge and infatuate Crawdaunt with its Ability Cute Charm.
Sapphire later also struggled against a potent counter Ability when she faced Brawly in Mashing Makuhita. After Rono was quickly defeated by Brawly's Makuhita, Chic used Flamethrower against Makuhita, but it had little effect due to its Thick Fat.
While on their way to Slateport City, Ruby and Sapphire were attacked by Courtney and Tabitha at the Abandoned Ship during Adding It Up with Plusle & Minun II. They escaped with the help of a wild Plusle and Minun after Ruby realized that their complimentary Abilities Plus and Minus greatly amplified their power when they fought together.
After Wattson is captured by the New Mauville generator, Sapphire devised a double battle strategy using his Electrike in Plugging Past Electrike II. While Electrike did not have the moves to defeat the generator itself, and the wild Donphan that Wattson and the Trick Master had originally intended to capture would be quickly eradicated by its powerful attacks, Electrike's Ability Lightning Rod would allow it to redirect the bolt away from Donphan, buying Donphan enough time to destroy the generator with Rollout.
Archie's Walrein activated Thick Fat during battle with Maxie's Camerupt in Walrein and Camerupt.
Norman's Spinda was revealed to have Own Tempo as its Ability in Rayquaza Redemption I but Skill Swapped it with his Slaking's Truant.

FireRed & LeafGreen chapter

Red's Aero activated Rock Head while using Take Down in Double Dealing with Deoxys. In the same chapter, Blue's Rhydon activated Lightning Rod.
Red's Poli activated Damp in Put Your Beast Foot Forward. It was Skill Swapped by Organism No. 2 in Storming the Forretress.
Blue's Alakazam copied Chuchu's Static with Role Play in Secrets from Sneasel.

Emerald chapter

Emerald's borrowed Phanpy had Pickup in A Dust-Up With Dusclops.

Diamond & Pearl chapter

Diamond's Lax had Pickup in Stagestruck Starly.
A wild Hippowdon had Sand Stream in Bombastic Bibarel & Heroic Hippopotas.
Cyrus's Magnezone had Magnet Pull in Problematic Probopass and Mad Magnezone II.
Diamond's Kit was revealed to have Own Tempo as its Ability in Well Met, Weepinbell but couldn't activate it since Sebastian's Weepinbell cancelled it out with Gastro Acid.

Platinum chapter

A Tyranitar belonging to the Battle Factory had Sand Stream in Outlasting Ledian.

In the Pokémon Diamond and Pearl Adventure manga

Hareta's Riolu has Steadfast which activated after flinching from B-2's Drapion.

Hareta's Piplup has Torrent, which powered up its Water-type moves.

Hareta's Luxio activated Intimidate in A Novel Test!! on Candice's Regirock and Regice but Regirock's Clear Body prevented Intimidate from working. Regice and Registeel were revealed to have Clear Body in the same chapter but weren't shown activating it.

Hareta's Regigigas has Slow Start, which proved to be a disadvantage for Hareta.

Koya's Absol's Super Luck nearly defeated Hareta's Empoleon but a comeback with Empoleon's Surf would have given Hareta the win but the battle was interrupted by Mitsumi's Glaceon's Ice Beam.

Koya's Mamoswine activated Snow Cloak during a hailstorm.

In the Pocket Monsters Platinum: Aim to Be Battle King!! manga

In PBK1, Shin's Bronzong had Heatproof to minimize the damage taken from Yū Shirogane's Infernape's Fire-type moves but Infernape's Blaze powered them back up.

Yū's Scizor received Heatran's Flash Fire Ability after Bronzong Skill Swapped them in PBK4. Yū's Bronzong had Levitate in that same chapter.